Filamentous Phages As a Model System in Soft Matter Physics

Dynamics of elongation of nematic tactoids in an electric field

Nematic tactoids are spindle-shaped droplets of a nematic phase nucleated in the co-existing isotropic phase. According to equilibrium theory, their internal structure and shape are controlled by a balance between the elastic deformation of the director field, induced by the preferred anchoring of that director field to the interface, and the interfacial free energy. Recent experiments on tactoids of chitin nanocrystals dispersed in water show that electrical fields can very strongly elongate tactoids, at least if the tactoids are sufficiently large in volume. However, this observation contradicts the predictions of equilibrium theory as well as findings from Monte Carlo simulations that do not show this kind of extreme elongation to take place at all. To explain this, we put forward a relaxational model based on the Oseen-Frank free energy of elastic deformation of a director field coupled to an anisotropic surface free energy. In our model, we use two reaction coordinates to describe the director field and the extent of elongation of the droplets and evaluate the evolution of both as a function of time following the switching on of an electric field. Depending on the relative magnitude of the fundamental relaxation rates associated with the two reaction coordinates, we find that the aspect ratio of the drops may develop a large and very long-lived overshoot before eventually relaxing to the much smaller equilibrium value. In that case, the response of the curvature of the director field lags behind, explaining the experimental observations. Our theory describes the experimental data reasonably well.

Shape Matters in Magnetic-Field-Assisted Assembly of Prolate Colloids

An anisotropic colloidal shape in combination with an externally tunable interaction potential results in a plethora of self-assembled structures with potential applications toward the fabrication of smart materials. Here we present our investigation on the influence of an external magnetic field on the self-assembly of hematite-silica core-shell prolate colloids for two aspect ratios ρ = 2.9 and 3.69. Our study shows a rather counterintuitive but interesting phenomenon, where prolate colloids self-assemble into oblate liquid crystalline (LC) phases. With increasing concentration, particles with smaller ρ reveal a sequence of LC phases involving para-nematic, nematic, smectic, and oriented glass phases. The occurrence of a smectic phase for colloidal ellipsoids has been neither predicted nor reported before. Quantitative shape analysis of the particles together with extensive computer simulations indicate that in addition to ρ, a subtle deviation from the ideal ellipsoidal shape dictates the formation of this unusual sequence of field-induced structures. Particles with ρ = 2.9 exhibit a hybrid shape containing features from both spherocylinders and ellipsoids, which make their self-assembly behavior richer than that observed for either of the "pure" shapes. The shape of the particles with higher ρ matches closely with the ideal ellipsoids, as a result their phase behavior follows the one expected for a "pure" ellipsoidal shape. Using anisotropic building blocks and external fields, our study demonstrates the ramifications of the subtle changes in the particle shape on the field-directed self-assembled structures with externally tunable properties.

Colloidal membranes of chiral rod-like particles

We study colloidal (or smectic) membranes composed of chiral rod-like particles through Monte Carlo simulations. These objects are formed due to the presence of Asakura-Oosawa spheres acting as depletants and creating an effective attraction between the rods. The membranes' shape and structure can be influenced by several parameters, e.g. the number of spheres and rods, their length and their interaction. In order to compare simulation results to an elastic theory, we follow two ansatzes, approximating the free elastic energy in different ways. Both of them lead to reasonable results and capture the behaviour of the colloidal membrane system. One approximation, however, is not suited for achiral rods, where twisting occurs due to surface energy rather than elastic energy. We extract the inverse cholesteric pitch and twist penetration depth for chiral rods with this approximation. The other one is used to introduce a complementary method to estimate elastic constants from the shape of colloidal membranes. Besides, we describe the transition from homogeneously twisted membranes to membranes composed of substructures that occur when the chiral interaction exceeds a length-dependent threshold. We believe that our detailed study and discussion of different aspects of this model system are valuable from a fundamental research viewpoint and suitable for material design suggestions.

Inducing Microscale Structural Order in Phage Nanofilament Hydrogels with Globular Proteins

Biological hydrogels play important physiological roles in the body. These hydrogels often contain ordered subdomains that provide mechanical toughness and other tissue-specific functionality. Filamentous bacteriophages are nanofilaments with a high aspect ratio that can self-assemble into liquid crystalline domains that could be designed to mimic ordered biological hydrogels and can thus find applications in biomedical engineering. We have previously reported hydrogels of pure cross-linked liquid crystalline filamentous phage formed at very high concentrations exhibiting a tightly packed microstructure and high stiffness. In this work, we report a method for inducing self-assembly of filamentous phage into liquid crystalline hydrogels at concentrations that are several orders of magnitude below that of lyotropic liquid crystal formation, thus creating structural order but a less densely packed microstructure. Hybrid hydrogels of M13 phage and bovine serum albumin (0.25 w/v%) were formed and shown to adsorb up to 16× their weight in water. Neither component gelled on its own at the low concentrations used, suggesting synergistic action between the two components in the formation of the hydrogel. The hybrid hydrogels exhibited repetitive self-healing under physiological conditions and at room temperature, autofluorescence in three channels, and antibacterial activity toward Escherichia coli host cells. Furthermore, the hybrid hydrogels exhibited a more than 2× higher ability to pack water compared to BSA-only hydrogels and 2× lower compression modulus compared to tightly packed M13-only hydrogels, suggesting that our method could be used to create hydrogels with tunable mechanical properties and pore structure through the addition of globular proteins, while maintaining bioactivity and microscale structural order.

Thin smectic liquid crystalline fibrils of chiral rodlike particles

Inspired by recent experimental work on virus-polymer mixtures, we study the properties of thin smectic fibrils composed of chiral rodlike particles using Monte Carlo simulations. Due to the interplay between surface energy, elastic deformation energy, and entropic effects, the fibril's layers relax into a twisted state. We focus our study on the layers' twist direction and map our results to the antiferromagnetic Ising model. In this view, the chiral interaction mimics an external field that drives the layers to have the same sense of twist. Besides, we determine the free energy difference and barrier height between an alternating and a nonalternating sequence of twisted layers composed of achiral rods and find that an alternating sequence is slightly preferred. We also see that the fibrils contract on increasing the chiral interaction strength and think that further studies on self-assembled functional materials can use our results.

Enhanced ordering in length-polydisperse carbon nanotube solutions at high concentrations as revealed by small angle X-ray scattering

Carbon nanotubes (CNTs) are stiff, all-carbon macromolecules with diameters as small as one nanometer and few microns long. Solutions of CNTs in chlorosulfonic acid (CSA) follow the phase behavior of rigid rod polymers interacting via a repulsive potential and display a liquid crystalline phase at sufficiently high concentration. Here, we show that small-angle X-ray scattering and polarized light microscopy data can be combined to characterize quantitatively the morphology of liquid crystalline phases formed in CNT solutions at concentrations from 3 to 6.5% by volume. We find that upon increasing their concentration, CNTs self-assemble into a liquid crystalline phase with a pleated texture and with a large inter-particle spacing that could be indicative of a transition to higher-order liquid crystalline phases. We explain how thermal undulations of CNTs can enhance their electrostatic repulsion and increase their effective diameter by an order of magnitude. By calculating the critical concentration, where the mean amplitude of undulation of an unconstrained rod becomes comparable to the rod spacing, we find that thermal undulations start to affect steric forces at concentrations as low as the isotropic cloud point in CNT solutions.

Filamentous Phages as Building Blocks for Bioactive Hydrogels

Filamentous bacteriophages (bacterial viruses) are semiflexible proteinous nanofilaments with high aspect ratios for which the surface chemistry can be controlled with atomic precision via genetic engineering. That, in addition to their ability to self-propagate and replicate a nearly monodisperse batch of biologically and chemically identical nanofilaments, makes these bionanofilaments superior to most synthetic nanoparticles and thus a powerful tool in the bioengineers' toolbox. Furthermore, filamentous phages form liquid crystalline structures at high concentrations; these ordered assemblies create hierarchically ordered macro-, micro-, and nanostructures that, once cross-linked, can form hierarchically ordered hydrogels, hydrated soft material with a variety of physical and chemical properties suitable for biomedical applications (e.g., wound dressings and tissue engineering scaffolds) as well as biosensing, diagnostic assays. We provide a critical review of these hydrogels of filamentous phage, and their physical, mechanical, chemical, and biological properties and current applications, as well as an overview of limitations and challenges and outlook for future applications. In addition, we present a list of design parameters for filamentous phage hydrogels to serve as a guide for the (bio)engineer and (bio)chemist interested in utilizing these powerful bionanofilaments for designing smart, bioactive materials and devices.

Application of Bacteriophages in Nanotechnology

Bacteriophages (phages for short) are viruses, which have bacteria as hosts. The single phage body virion, is a colloidal particle, often possessing a dipole moment. As such, phages were used as perfectly monodisperse systems to study various physicochemical phenomena (e.g., transport or sedimentation in complex fluids), or in the material science (e.g., as scaffolds). Nevertheless, phages also execute the life cycle to multiply and produce progeny virions. Upon completion of the life cycle of phages, the host cells are usually destroyed. Natural abilities to bind to and kill bacteria were a starting point for utilizing phages in phage therapies (i.e., medical treatments that use phages to fight bacterial infections) and for bacteria detection. Numerous applications of phages became possible thanks to phage display-a method connecting the phenotype and genotype, which allows for selecting specific peptides or proteins with affinity to a given target. Here, we review the application of bacteriophages in nanoscience, emphasizing bio-related applications, material science, soft matter research, and physical chemistry.

Novel Trends in Lyotropic Liquid Crystals

We introduce and shortly summarize a variety of more recent aspects of lyotropic liquid crystals (LLCs), which have drawn the attention of the liquid crystal and soft matter community and have recently led to an increasing number of groups studying this fascinating class of materials, alongside their normal activities in thermotopic LCs. The diversity of topics ranges from amphiphilic to inorganic liquid crystals, clays and biological liquid crystals, such as viruses, cellulose or DNA, to strongly anisotropic materials such as nanotubes, nanowires or graphene oxide dispersed in isotropic solvents. We conclude our admittedly somewhat subjective overview with materials exhibiting some fascinating properties, such as chromonics, ferroelectric lyotropics and active liquid crystals and living lyotropics, before we point out some possible and emerging applications of a class of materials that has long been standing in the shadow of the well-known applications of thermotropic liquid crystals, namely displays and electro-optic devices.

Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections

Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships with their bacterial hosts that impact both bacterial phenotypes and chronic infection. We and others have reported that Pf phages are a virulence factor that promote the pathogenesis of P. aeruginosa infections in animal models and are associated with worse skin and lung infections in humans. Here we review the biology of Pf phage and what is known about its contributions to pathogenesis and clinical disease. First, we review the structure, genetics, and epidemiology of Pf phage. Next, we address the diverse and surprising ways that Pf phages contribute to P. aeruginosa phenotypes including effects on biofilm formation, antibiotic resistance, and motility. Then, we cover data indicating that Pf phages suppress mammalian immunity at sites of bacterial infection. Finally, we discuss recent literature implicating Pf in chronic P. aeruginosa infections in CF and other settings. Together, these reports suggest that Pf bacteriophage have direct effects on P. aeruginosa infections and that temperate phages are an exciting frontier in microbiology, immunology, and human health.

Polymers with controlled assembly and rigidity made with click-functional peptide bundles

The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including chemical recognition (of enzyme substrates or adhesive ligands¹, for instance), exquisite nanostructures (composed of peptides², proteins³ or nucleic acids⁴), and unusual mechanical properties (such as silk-like strength³, stiffness⁵, viscoelasticity⁶ and resiliency⁷). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical 'click' covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or 'bundlemers', can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Furthermore, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural 'click' chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.

Non-lytic M13 phage-based highly sensitive impedimetric cytosensor for detection of coliforms

A highly sensitive and selective non-lytic M13 phage-based electrochemical impedance spectroscopy (EIS) cytosensor for early detection of coliforms is introduced for the first time. Gold nanoparticles were electrochemically deposited on the surface of glassy carbon electrode, and the M13 phage particles were immobilized on them using 3-mercaptopropionic acid linker and zero-length crosslinking chemistry (EDC/NHS). Next, the sensor surface was blocked to avoid non-specific binding. The M13-EIS cytosensor was tested for detection of F⁺ pili Escherichia coli species, using XL1-Blue and K12 strains, as examples of coliforms. The selectivity against non-host strains was demonstrated using Pseudomonas Chlororaphis. The binding of E. coli to the M13 phage on the cytosensor surface increased the charge transfer resistance, enabling detection of coliforms. The biosensor achieved a limit of detection (LOD) of 14 CFU/mL, the lowest reported to-date using EIS-phage sensors, and exhibited a high selectivity towards the tested coliforms. The SEM micrographs confirmed the successful capturing of E. coli on the M13-based EIS cytosensor. Moreover, the sensor showed almost the same sensitivity in the simulated river water samples as in phosphate buffer, reflecting its applicability to real samples. On the other hand, this sensor system exhibited high stability under harsh environmental conditions of pH (3.0-10.0) and temperature as high as 45 °C for up to two weeks. Overall, this sensor system has excellent potential for real field detection of fecal coliforms.

Filamentous phages as building blocks for reconfigurable and hierarchical self-assembly

Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties of diameter, length, rigidity, charge and chirality. Engineering these viruses leads to a library of colloidal rods, which can be used as building blocks for reconfigurable and hierarchical self-assembly. Their condensation in an aqueous solution with additive polymers, which act as depletants to induce attraction between the rods, leads to a myriad of fluid-like micronic structures ranging from isotropic/nematic droplets, colloid membranes, achiral membrane seeds, twisted ribbons, π-wall, pores, colloidal skyrmions, Möbius anchors, scallop membranes to membrane rafts. These structures, and the way that they shape-shift, not only shed light on the role of entropy, chiral frustration and topology in soft matter, but also mimic many structures encountered in different fields of science. On the one hand, filamentous phages being an experimental realization of colloidal hard rods, their condensation mediated by depletion interactions constitutes a blueprint for the self-assembly of rod-like particles and provides a fundamental foundation for bio- or material-oriented applications. On the other hand, the chiral properties of the viruses restrict the generalities of some results but vastly broaden the self-assembly possibilities.

Conformations and membrane-driven self-organization of rodlike fd virus particles on freestanding lipid membranes

Membrane-mediated interactions and aggregation of colloidal particles adsorbed to responsive elastic membranes are challenging problems relevant for understanding the microscopic organization and dynamics of biological membranes. We experimentally study the behavior of rodlike semiflexible fd virus particles electrostatically adsorbed to freestanding cationic lipid membranes and find that their behavior can be controlled by tuning the membrane charge and ionic strength of the surrounding medium. Three distinct interaction regimes of rodlike virus particles with responsive elastic membranes can be observed. (i) A weakly charged freestanding cationic lipid bilayer in a low ionic strength medium represents a gentle quasi-2D substrate preserving the integrity, structure, and mechanical properties of the membrane-bound semiflexible fd virus, which under these conditions is characterized by a monomer length of 884 ± 4 nm and a persistence length of 2.5 ± 0.2 μm, in perfect agreement with its properties in bulk media. (ii) An increase in the membrane charge leads to the membrane-driven collapse of fd virus particles on freestanding lipid bilayers and lipid nanotubes into compact globules. (iii) When the membrane charge is low, and the mutual electrostatic repulsion of membrane-bound virus particles is screened to a considerable degree, membrane-driven self-organization of membrane-bound fd virus particles into long linear tip-to-tip aggregates showing dynamic self-assembly/disassembly and quasi-semiflexible behavior takes place. These observations are in perfect agreement with the results of recent theoretical and simulation studies predicting that membrane-mediated interactions can control the behavior of colloidal particles adsorbed on responsive elastic membranes.

Attractive and repulsive polymer-mediated forces between scale-free surfaces

We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if some or all surfaces are covered by adsorbing layers). The strength and sign of the force in general depends on the detailed shape and adsorption properties of the obstacles but assumes simple universal forms if characteristic length scales associated with the objects are large. This occurs for scale-free shapes (such as a flat plate, straight wire, or cone) when the polymer is repelled by the obstacles or is marginally attracted to it (close to the depinning transition where the absorption length is infinite). In such cases, the separation h between obstacles is the only relevant macroscopic length scale, and the polymer-mediated force equals Ak_{B}T/h, where T is temperature. The amplitude A is akin to a critical exponent, depending only on geometry and universality of the polymer system. The value of A, which we compute for simple geometries and ideal polymers, can be positive or negative. Remarkably, we find A=0 for ideal polymers at the adsorption transition point, irrespective of shapes of the obstacles, i.e., at this special point there is no polymer-mediated force between obstacles (scale free or not).

Twisting with a twist: supramolecular helix fluctuations in chiral nematics

Most theoretical descriptions of lyotropic cholesteric liquid crystals to date focus on homogeneous systems in which the rod concentration, as opposed to the rod orientation, is uniform. In this work, we build upon the Onsager-Straley theory for twisted nematics and study the effect of weak concentration gradients, generated by some external potential, on the cholesteric twist. We apply our theory to chiral nematics of nanohelices in which the supramolecular helix sense is known to spontaneously change sign upon variation of particle concentration, passing through a so-called compensation point at which the mesoscopic twist vanishes. We show that the imposed field offers exquisite control of the handedness and magnitude of the helicoidal director field, even at weak field strengths. Within the same framework we also quantify the director fluctuation spectrum and find evidence for a correlation length diverging at the compensation point.

Filamentous Phage: Structure and Biology

Ff filamentous phage (fd, M13 and f1) of Escherichia coli have been the workhorse of phage display technology for the past 30 years. Dominance of Ff over other bacteriophage in display technology stems from the titres that are about 100-fold higher than any other known phage, efficacious transformation ensuring large library size and superior stability of the virion at high temperatures, detergents and pH extremes, allowing broad range of biopanning conditions in screening phage display libraries. Due to the excellent understanding of infection and assembly requirements, Ff phage have also been at the core of phage-assisted continual protein evolution strategies (PACE). This chapter will give an overview of the Ff filamentous phage structure and biology, emphasizing those properties of the Ff phage life cycle and virion that are pertinent to phage display applications.